Counting Motifs In Proteins

Question

[Nitin]

hi all,

I protein sequences in text file as follows

> P1
MPPRRSIVEVKVLDVQKRRVPNKHYVYIIRVTWSSGATEAIYRRYSKFFDLQMQMLDKFP
MEGGQKDPKQRIIPFLPGKILFRRSHIRDVAVKRLIPIDEYCKALIQLPPYISQCDEVLQ
FFETRPEDLNPPKEEHIGKKKSGNDPTSVDPMVLEQYVVVADYQKQESSEISLSVGQVVD
IIEKNESGWWFVSTAEEQGWVPATCLEGQDGVQDEFSLQPEEEEKYTVIYPYTARDQDEM
NLERGAVVEVVQKNLEGWWKIRYQGKEGWAPASYLKKNSGEPLPPKLGPSSPAHSGALDL
DGVSRHQNAMGREKELLNNQRDGRFEGRLVPDGDVKQRSPKMRQRPPPRRDMTIPRGLNL

>P2
MAEVRKFTKRLSKPGTAAELRQSVSEAVRGSVVLEKAKLVEPLDYENVITQRKTQIYSDP
LRDLLMFPMEDISISVIGRQRRTVQSTVPEDAEKRAQSLFVKECIKTYSTDWHVVNYKYE
DFSGDFRMLPCKSLRPEKIPNHVFEIDEDCEKDEDSSSLCSQKGGVIKQGWLHKANVNST
ITVTMKVFKRRYFYLTQLPDGSYILNSYKDEKNSKESKGCIYLDACIDVVQCPKMRRHAF
ELKMLDKYSHYLAAETEQEMEEWLIMLKKIIQINTDSLVQEKKDTVEAIQEEETSSQGKA
ENIMASLERSMHPELMKYGRETEQLNKLSRGDGRQNLFSFDSEVQRLDFSGIEPDVKPFE
EKCNKRFMVNCHDLTFNILGHIGDNAKGPPTNVEPFFINLALFDVKNNCKISADFHVDLN
PPSVREMLWGTSTQLSNDGNAKGFSPESLIHGIAESQLCYIKQGIFSVTNPHPEIFLVVR

>P3
GDDSEWLKLPVDQKCEHKLWKARLSGYEEALKIFQKIKDEKSPEWSKYLGLIKKFVTDS
NAVVQLKGLEAALVYVENAHVAGKTTGEVVSGVVSKVFNQPKAKAKELGIEICLMYVEIE
KGESVQEELLKGLDNKNPKIIVACIETLRKALSEFGSKIISLKPIIKVLPKLFESRDKAV
RDEAKLFAIEIYRWNRDAVKHTLQNINSVQLKELEEEWVKLPTGAPKPSRFLRSQQELEA
KLEQQQSAGGDAEGGGDDGDEVPQVDAYELLDAVEILSKLPKDFYDKIEAKKWQERKEAL
EAVEVLVKNPKLEAGDYADLVKALKKVVGKDTNVMLVALAAKCLTGLAVGLRKKFGQYAG
HVVPTILEKFKEKKPQVVQALQEAIDAIFLTTTLQNISEDVLAVMDNKNPTIKQQTSLFI
ARSFRHCTSSTLPKSLLKPFCAALLKHINDSAPEVRDAAFEALGTALKVVGEKSVNPFLA

...

in total 100 sequences In these sequences i searched a motif of interest using python script as follows

import re
infile=open("seq.fasta",'r')
out=open("results.csv",'w')
pattern=re.compile(r"(P[A-Z]{2}P)")
for line in infile:
   line = line.strip("\n")
   if line.startswith('>'):
      name=line
   else:      
      s = re.findall(pattern,line)
      print '%s:%s' %(name,s)
      out.write('%s:\t%s\n' %(name,s))

This script perfectly worked it gave me desired motif i wanted...now i wanted to count motif of interest in each seqeunce present out put of the script is as follows

>p1: 
PGCP

>p1: 
PHCP,
PKCP

and so on

but I want out put as follows

>p1:
1

>p1: 
2

Can anybody tell me how to do this using python?

Thanks in Advance

Ni

Answer 1

[Giovanni M Dall'Olio]

You are very close... Just notice that you can get the total number of occurrences by looking at the length of "s".

For example:

print '%s:%s (%s hits)' %(name,s, len(s))

instead of

print '%s:%s' %(name,s)

Answer 2

[Niallhaslam]

You may also be interested in the SLiMSearch software described here. It allows you to search for regular expressions in protein sequences. Video lecture.

Software available here: http://www.soton.ac.uk/~re1u06/software/slimsuite/